SeuratObject: Data Structures for Single Cell Data

Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for more details.

Version: 5.0.1
Depends: R (≥ 4.0.0), sp (≥ 1.5.0)
Imports: future, future.apply, grDevices, grid, Matrix (≥ 1.6.3), methods, progressr, Rcpp (≥ 1.0.5), rlang (≥ 0.4.7), stats, tools, utils, spam, lifecycle, generics
LinkingTo: Rcpp, RcppEigen
Suggests: DelayedArray, fs (≥ 1.5.2), ggplot2, HDF5Array, rmarkdown, testthat, BPCells, sf (≥ 1.0.0)
Enhances: Seurat
Published: 2023-11-17
Author: Rahul Satija ORCID iD [aut], Paul Hoffman ORCID iD [aut, cre], Yuhan Hao ORCID iD [aut], Austin Hartman ORCID iD [aut], Gesmira Molla ORCID iD [aut], Andrew Butler ORCID iD [aut], Tim Stuart ORCID iD [aut], Madeline Kowalski ORCID iD [ctb], Saket Choudhary ORCID iD [ctb], Skylar Li [ctb], Longda Jiang ORCID iD [ctb], Jeff Farrell [ctb], Shiwei Zheng ORCID iD [ctb], Christoph Hafemeister ORCID iD [ctb], Patrick Roelli [ctb]
Maintainer: Paul Hoffman <seurat at nygenome.org>
BugReports: https://github.com/mojaveazure/seurat-object/issues
License: MIT + file LICENSE
URL: https://mojaveazure.github.io/seurat-object/, https://github.com/mojaveazure/seurat-object
NeedsCompilation: yes
Additional_repositories: https://bnprks.r-universe.dev
Materials: NEWS
In views: Omics
CRAN checks: SeuratObject results

Documentation:

Reference manual: SeuratObject.pdf

Downloads:

Package source: SeuratObject_5.0.1.tar.gz
Windows binaries: r-devel: SeuratObject_5.0.1.zip, r-release: SeuratObject_5.0.1.zip, r-oldrel: SeuratObject_5.0.1.zip
macOS binaries: r-release (arm64): SeuratObject_5.0.1.tgz, r-oldrel (arm64): SeuratObject_5.0.1.tgz, r-release (x86_64): SeuratObject_5.0.1.tgz
Old sources: SeuratObject archive

Reverse dependencies:

Reverse depends: SCArray.sat, Seurat, tidyseurat
Reverse imports: bbknnR, CAMML, CDI, CuratedAtlasQueryR, GeomxTools, mastR, Platypus, scaper, sccomp, scCustomize, scpoisson, scRepertoire, scRNAseqApp, Signac, SpatialDecon
Reverse suggests: cellpypes, CoGAPS, CytoSimplex, DCATS, edgeR, escape, ggsc, MOFA2, Nebulosa, RESET, rliger, scOntoMatch, SCpubr, SimBu, singleCellHaystack, singleCellTK, SpaTopic, SPECK, SPOTlight, VAM

Linking:

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